• Universiteitssingel50, UNS50

    6229 ER Maastricht

    Netherlands

Research Output

Abstract

Open PHACTS: Meaningful linking of preclinical drug discovery knowledge

Willighagen, E. L., Brenninkmeijer, C., Evelo, C. T., Harland, L., Gray, A. J. G., Goble, C., Waagmeester, A. S. & Williams, A. J., 1 Jan 2013.

Research output: Contribution to conferenceAbstractAcademic

Semantic annotation of PubChem databases

Fu, G., Batchelor, C., Dumontier, M., Hastings, J., Kuecuek, H., Schurer, S. C., Vempati, U., Willighagen, E. & Bolton, E., 8 Sep 2013.

Research output: Contribution to conferenceAbstractAcademic

Article

2D-electrophoresis and multiplex immunoassay proteomic analysis of different body fluids and cellular components reveal known and novel markers for extended fasting

Bouwman, F. G., de Roos, B., Rubio Aliaga, I., Crosley, L. K., Duthie, S. J., Mayer, C., Horgan, G., Polley, A. C., Heim, C., Coort, S. L. M., Evelo, C. T. A., Mulholland, F., Johnson, I. T., Elliott, R. M., Daniel, H. & Mariman, E. C., 1 Jan 2011, In : BMC Medical Genomics. 4, 1, p. 24

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
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A bioinformatics workflow to decipher transcriptomic data from vitamin D studies

Muñoz García, A., Eijssen, L. M., Kutmon, M., Sarathy, C., Cengo, A., Hewison, M., Evelo, C. T., Lenz, M. & Coort, S. L., May 2019, In : Journal of Steroid Biochemistry and Molecular Biology. 189, p. 28-35 8 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

A combined transcriptomics and lipidomics analysis of subcutaneous, epididymal and mesenteric adipose tissue reveals marked functional differences

Caesar, R., Manieri, M., Kelder, T. A. J., Boekschoten, M., Evelo, C. T. A., Muller, M., Kooistra, T., Cinti, S., Kleemann, R. & Drevon, C. A., 12 Jul 2010, In : PLOS ONE. 5, 7, 14 p., e11525.

Research output: Contribution to journalArticleAcademicpeer-review

A Data Fusion Pipeline for Generating and Enriching Adverse Outcome Pathway Descriptions

Nymark, P., Rieswijk, L., Ehrhart, F., Jeliazkova, N., Tsiliki, G., Sarimveis, H., Evelo, C. T., Hongisto, V., Kohonen, P., Willighagen, E. & Grafstrom, R. C., Mar 2018, In : Toxicological Sciences. 162, 1, p. 264-275 12 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
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Open Access

A dual transcript-discovery approach to improve the delimitation of gene features from RNA-seq data in the chicken model

Orgeur, M., Martens, M., Boerno, S. T., Timmermann, B., Duprez, D. & Stricker, S., Jan 2018, In : Biology Open. 7, 1, p. 1-8 8 p., 028498.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Adverse outcome pathways: opportunities, limitations and open questions

Leist, M., Ghallab, A., Graepel, R., Marchan, R., Hassan, R., Bennekou, S. H., Limonciel, A., Vinken, M., Schildknecht, S., Waldmann, T., Danen, E., van Ravenzwaay, B., Kamp, H., Gardner, I., Godoy, P., Bois, F. Y., Braeuning, A., Reif, R., Oesch, F., Drasdo, D. & 33 others, Hoehme, S., Schwarz, M., Hartung, T., Braunbeck, T., Beltman, J., Vrieling, H., Sanz, F., Forsby, A., Gadaleta, D., Fisher, C., Kelm, J., Fluri, D., Ecker, G., Zdrazil, B., Terron, A., Jennings, P., van der Burg, B., Dooley, S., Meijer, A. H., Willighagen, E., Martens, M., Evelo, C., Mombelli, E., Taboureau, O., Mantovani, A., Hardy, B., Koch, B., Escher, S., van Thriel, C., Cadenas, C., Kroese, D., van de Water, B. & Hengstler, J. G., Nov 2017, In : Archives of Toxicology. 91, 11, p. 3477-3505 29 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
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496 Downloads (Pure)

Alterations in hepatic one-carbon metabolism and related pathways following a high-fat dietary intervention

Rubio-Aliaga, I., de Roos, B., Sailer, M., McLoughlin, G. A., Boekschoten, M. V., van Erk, M., Bachmair, E. M., van Schothorst, E. M., Keijer, J., Coort, S. L. M., Evelo, C. T. A., Gibney, M. J., Daniel, H., Muller, M., Kleemann, R. & Brennan, L., 1 Jan 2011, In : Physiological genomics. 43, 8, p. 408-416

Research output: Contribution to journalArticleAcademicpeer-review

Altered gene expression in human placentas after IVF/ICSI

Nelissen, E. C. M., Dumoulin, J. C. M., Busato, F., Ponger, L., Eijssen, L. M., Evers, J. L. H., Tost, J. & van Montfoort, A. P. A., Dec 2014, In : Human Reproduction. 29, 12, p. 2821-2831 11 p.

Research output: Contribution to journalArticleAcademicpeer-review

Altered myocardial gene expression reveals possible maladaptive processes in heterozygous and homozygous cardiac myosin-binding protein C knockout mice.

Eijssen, L. M. T., van den Bosch, B. J. C., Vignier, N., Lindsey, P. J., van den Burg, C. M. M., Carrier, L., Doevendans, P. A. F. M., van der Vusse, G. J. & Smeets, H. J., 1 Jan 2008, In : Genomics. 91, 1, p. 52-60

Research output: Contribution to journalArticleAcademicpeer-review

Alzheimer's disease-associated (hydroxy)methylomic changes in the brain and blood

Lardenoije, R., Roubroeks, J. A. Y., Pishva, E., Leber, M., Wagner, H., Iatrou, A., Smith, A. R., Smith, R. G., Eijssen, L. M. T., Kleineidam, L., Kawalia, A., Hoffmann, P., Luck, T., Riedel-Heller, S., Jessen, F., Maier, W., Wagner, M., Hurlemann, R., Kenis, G., Ali, M. & 9 others, del Sol, A., Mastroeni, D., Delvaux, E., Coleman, P. D., Mill, J., Rutten, B. P. F., Lunnon, K., Ramirez, A. & van den Hove, D. L. A., 27 Nov 2019, In : Clinical epigenetics. 11, 1, 15 p., 164.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

A network biology workflow to study transcriptomics data of the diabetic liver

Kutmon, M., Evelo, C. T. & Coort, S. L., 1 Jan 2014, In : BMC Genomics. 15, p. 971

Research output: Contribution to journalArticleAcademicpeer-review

An evaluation of two-channel ChIP-on-chip and DNA methylation microarray normalization strategies

Michiel Adriaens, M. E., Jaillard, M. N. L., Eijssen, L. M. T., Mayer, C. D. & Evelo, C. T. A., 25 Jan 2012, In : BMC Genomics. 13, 1, p. 42 14 p., 42.

Research output: Contribution to journalArticleAcademicpeer-review

An integrated bioinformatics approach to improve two-color microarray quality-control: impact on biological conclusions.

van Haaften, R. I., Luceri, C., van Erk, A. & Evelo, C. T., 1 Jan 2009, In : Genes and nutrition. 4, 2, p. 123-127

Research output: Contribution to journalArticleAcademicpeer-review

A novel stepwise analysis procedure of genome-wide expression profiles identifies transcript signatures of thiamine genes as classifiers of mitochondrial mutants.

Eijssen, L. M. T., Lindsey, P. J., Peeters, R., Westra, R. L., van Eijsden, R. G. E., Bolotin-Fukuhara, M., Smeets, H. J. & Vlietinck, R. F. M., 1 Jan 2008, In : Yeast. 25, 2, p. 129-140

Research output: Contribution to journalArticleAcademicpeer-review

Answering biological questions: querying a systems biology database for nutrigenomics

Evelo, C. T. A., van Bochove, G. S. & Saito, J. T., Feb 2011, In : Genes and nutrition. 6, 1, p. 81-87 7 p.

Research output: Contribution to journalArticleAcademicpeer-review

A pathway approach to investigate the function and regulation of SREBPs.

Daemen, S., Kutmon, M. & Evelo, C. T. A., 1 Jan 2013, In : Genes and nutrition. 8, 3, p. 289-300

Research output: Contribution to journalArticleAcademicpeer-review

Applications of the InChI in cheminformatics with the CDK and Bioclipse.

Spjuth, O., von Berg, A., Adams, S. & Willighagen, E. L., 13 Mar 2013, In : Journal of Cheminformatics. 5, 1, p. 14 7 p., 14.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Applying linked data approaches to pharmacology: Architectural decisions and implementation

Gray, A. J. G., Groth, P., Loizou, A., Askjaer, S., Brenninkmeijer, C., Burger, K., Chichester, C., Evelo, C. T., Goble, C., Harland, L., Pettifer, S., Thompson, M., Waagmeester, A. & Williams, A. J., 1 Jan 2014, In : Semantic web. 5, 2, p. 101-113 13 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

A simple and efficient toolset for analysing mitochondrial trafficking in neuronal cells

Shahen, V. A., Cantrill, L. C., Bahram Sangani, N., Christodoulou, J. & Gold, W. A., 1 Jan 2018, In : Acta Histochemica. 120, 8, p. 797-805 9 p.

Research output: Contribution to journalArticleAcademicpeer-review

A survey of quantitative descriptions of molecular structure

Guha, R. & Willighagen, E., Sep 2012, In : Current Topics in Medicinal Chemistry. 12, 18, p. 1946-1956 11 p.

Research output: Contribution to journalArticleAcademicpeer-review

A transcriptomics data-driven gene space accurately predicts liver cytopathology and drug-induced liver injury

Kohonen, P., Parkkinen, J. A., Willighagen, E. L., Ceder, R., Wennerberg, K., Kaski, S. & Grafstrom, R. C., 3 Jul 2017, In : Nature Communications. 8, 15 p., 15932.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

A user-friendly workflow for analysis of Illumina gene expression bead array data available at the arrayanalysis.org portal

Eijssen, L. M. T., Goelela, V. S., Kelder, T., Adriaens, M. E., Evelo, C. T. & Radonjic, M., 1 Jan 2015, In : BMC Genomics. 16, 482.

Research output: Contribution to journalArticleAcademicpeer-review

Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment

Bohler, A., Eijssen, L. M., van Iersel, M. P., Leemans, C., Willighagen, E. L., Kutmon, M., Jaillard, M. & Evelo, C. T., 1 Jan 2015, In : BMC Bioinformatics. 16, 267.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Beyond Pathway Analysis: Identification of Active Subnetworks in Rett Syndrome

Miller, R. A., Ehrhart, F., Eijssen, L. M. T., Slenter, D. N., Curfs, L. M. G., Evelo, C. T., Willighagen, E. L. & Kutmon, M., 21 Feb 2019, In : Frontiers in Genetics. 10, 10 p., 59.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Bilberries potentially alleviate stress-related retinal gene expression induced by a high-fat diet in mice

Mykkanen, O. T., Kalesnykas, G., Adriaens, M., Evelo, C. T., Torronen, R. & Kaarniranta, K., 7 Sep 2012, In : Molecular Vision. 18, 247, p. 2338-2351 14 p.

Research output: Contribution to journalArticleAcademicpeer-review

Bioclipse-R: integrating management and visualization of life science data with statistical analysis

Spjuth, O., Georgiev, V., Carlsson, L., Alvarsson, J., Berg, A., Willighagen, E., Wikberg, J. E. & Eklund, M., 1 Jan 2013, In : Bioinformatics. 29, 2, p. 286-289

Research output: Contribution to journalArticleAcademicpeer-review

Bioinformatic interrogation of expression array data to identify nutritionally regulated genes potentially modulated by DNA methylation

McKay, J. A., Michiel Adriaens, M. E., Ford, D., Relton, C. L., Evelo, C. T. & Mathers, J. C., 1 Jan 2008, In : Genes and nutrition. 3, 3-4, p. 167-71

Research output: Contribution to journalArticleAcademicpeer-review

Bioinformatics for the NuGO proof of principle study: analysis of gene expression in muscle of ApoE3*Leiden mice on a high-fat diet using PathVisio

Coort, S. L., van Iersel, M. P., van Erk, M., Kooistra, T., Kleemann, R. & Evelo, C. T., 1 Jan 2008, In : Genes and nutrition. 3, 3-4, p. 185-91

Research output: Contribution to journalArticleAcademicpeer-review

Biologically relevant effects of mRNA amplification on gene expression profiles

van Haaften, R. I. M., Schroen, B. L., Janssen, B. J., van Erk, A. A., Debets, J. J., Smeets, H. J., Smits, J. F., van den Wijngaard, A., Pinto, Y. M. & Evelo, C. T., 1 Jan 2006, In : BMC Bioinformatics. 7, p. 200

Research output: Contribution to journalArticleAcademicpeer-review

Biological pathways leading from ANGPTL8 to Diabetes Mellitus: a co-expression network based analysis

Siddiqa, A., Cirillo, E., Tareen, S. H. K., Ali, A., Kutmon, M., Eijssen, L. M. T., Ahmad, J., Evelo, C. T. & Coort, S. L., 21 Dec 2018, In : Frontiers in physiology. 9, 15 p., 1841.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Biotransformation pathway maps in WikiPathways enable direct visualization of drug metabolism related expression changes.

Jennen, D. G. J., Gaj, S., Giesbertz, P. J., van Delft, J. H. M., Evelo, C. T. A. & Kleinjans, J. C. S., 1 Jan 2010, In : Drug Discovery Today. 15, 19-20, p. 851-858

Research output: Contribution to journalArticleAcademicpeer-review

Blue Obelisk - Interoperability in chemical informatics

Guha, R., Howard, MT., Hutchison, GR., Murray-Rust, P., Rzepa, H., Steinbeck, C., Wegner, J. & Willighagen, EL., May 2006, In : Journal of Chemical Information and Modeling. 46, 3, p. 991-998 8 p.

Research output: Contribution to journalArticleAcademicpeer-review

Cardiac contractile dysfunction in insulin-resistant rats fed a high-fat diet is associated with elevated CD36-mediated fatty acid uptake and esterification

Ouwens, DM., Diamant, M., Fodor, M., Habets, D. D. J., Pelsers, M. M. A. L., El Hasnaoui, M. M., Dang, Z. C., van den Brom, C. E., Vlasblom, R., Rietdijk, A., Boer, C., Coort, S. L. M., Glatz, J. F. & Luiken, J. J. F. P., 1 Jan 2007, In : Diabetologia. 50, 9, p. 1938-48

Research output: Contribution to journalArticleAcademicpeer-review

Cardiac substrate uptake and metabolism in obesity and type-2 diabetes: Role of sarcolemmal substrate transporters

Coort, S. L. M., Bonen, A., van der Vusse, G. J., Glatz, J. F. & Luiken, J. J. F. P., 1 Jan 2007, In : Molecular and Cellular Biochemistry. 299, 1-2, p. 5-18

Research output: Contribution to journalArticleAcademicpeer-review

Challenges in evaluating the oculomotor function in individuals with Rett syndrome using electronystagmography

de Breet, L. H. M., Townend, G. S., Curfs, L. M. G., Kingma, H., Smeets, E. E. J., Lucieer, F., Widdershoven, J. & van de Berg, R., Mar 2019, In : European Journal of Paediatric Neurology. 23, 2, p. 262-269 8 p.

Research output: Contribution to journalArticleAcademicpeer-review

Challenges of molecular nutrition research 6: the nutritional phenotype database to store, share and evaluate nutritional systems biology studies

van Ommen, B., Bouwman, J., Dragsted, L. O., Drevon, C. A., Elliott, R., de Groot, P., Kaput, J., Mathers, J. C., Muller, M., Pepping, F., Saito, J. T., Scalbert, A., Radonjic, M., Rocca Serra, P., Travis, A., Wopereis, S. & Evelo, C. T. A., 1 Jan 2010, In : Genes and nutrition. 5, 3, p. 189-203

Research output: Contribution to journalArticleAcademicpeer-review

Changing computational research. The challenges ahead

Neylon, C., Aerts, J., Brown, C. T., Coles, S. J., Hatton, L., Lemire, D., Millman, K. J., Murray-Rust, P., Perez, F., Saunders, N., Shah, N., Smith, A., Varoquaux, G. & Willighagen, E., 1 Jan 2012, In : Source code for biology and medicine. 7, 1, p. 2

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Cheminformatics

Wegner, J. K., Sterling, A., Guha, R., Bender, A., Faulon, J. L., Hastings, J., O'Boyle, N., Overington, J., Van Vlijmen, H. & Willighagen, E., 1 Jan 2012, In : Communications of the Acm. 55, 11, p. 65-75

Research output: Contribution to journalArticleAcademicpeer-review

Childhood asthma: exhaled markers of airway inflammation, asthma control score, and lung function tests

Rosias, P. P. R., Dompeling, E. D., Dentener, M. A., Pennings, H. J., Hendriks, H., van Iersel, M. P. & Jöbsis, Q., 1 Jan 2004, In : Pediatric Pulmonology. 38, 2, p. 107-114

Research output: Contribution to journalArticleAcademicpeer-review

Chip-based mtDNA mutation screening enables fast and reliable genetic diagnosis of OXPHOS patients

van Eijsden, R. G., Gerards, M., Eijssen, L. M., Hendrickx, A. T., Jongbloed, R. J. E., Wokke, J. H., Hintzen, R. Q., Rubio-Gozalbo, M. E., De Coo, I. F., Briem, E., Tiranti, V. & Smeets, H. J., 1 Jan 2006, In : Genetics in Medicine. 8, 10, p. 620-627

Research output: Contribution to journalArticleAcademicpeer-review

Circulating Serum MicroRNAs as Potential Diagnostic Biomarkers of Posttraumatic Stress Disorder: A Pilot Study

Snijders, C., Krauskopf, J., Pishva, E., Eijssen, L., Machiels, B., Kleinjans, J., Kenis, G., van den Hove, D., Kim, M. O., Boks, M. P. M., Vinkers, C. H., Vermetten, E., Geuze, E., Rutten, B. P. F. & de Nijs, L., 22 Nov 2019, In : Frontiers in Genetics. 10, 10 p., 1042.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Classification of mild cognitive impairment and Alzheimer's Disease with machine-learning techniques using H-1 Magnetic Resonance Spectroscopy data

Munteanu, C., Fernandez-Lozano, C., Mato Abad, V., Pita Fernandez, S., Alvarez-Linera, J., Antonio Hernandez-Tamames, J. & Pazos, A., 1 Jan 2015, In : Expert Systems with Applications. 42, 15-16, p. 6205-6214

Research output: Contribution to journalArticleAcademicpeer-review

Classification of signaling proteins based on molecular star graph descriptors using Machine Learning models

Fernandez-Lozano, C., Cuinas, R. F., Seoane, J. A., Fernandez-Blanco, E., Dorado, J. & Munteanu, C., 1 Jan 2015, In : Journal of Theoretical Biology. 384, p. 50-58

Research output: Contribution to journalArticleAcademicpeer-review

Comment: The FAIR Guiding Principles for scientific data management and stewardship

Wilkinson, M. D., Dumontier, M., Aalbersberg, IJ. J., Appleton, G., Axton, M., Baak, A., Blomberg, N., Boiten, J-W., Santos, L. B. D. S., Bourne, P. E., Bouwman, J., Brookes, A. J., Clark, T., Crosas, M., Dillo, I., Dumon, O., Edmunds, S., Evelo, C. T., Finkers, R., Gonzalez-Beltran, A. & 33 others, Gray, A. J. G., Groth, P., Goble, C., Grethe, J. S., Heringa, J., 't Hoen, P. A. C., Hooft, R., Kuhn, T., Kok, R., Kok, J., Lusher, S. J., Martone, M. E., Mons, A., Packer, A. L., Persson, B., Rocca-Serra, P., Roos, M., van Schaik, R., Sansone, S-A., Schultes, E., Sengstag, T., Slater, T., Strawn, G., Swertz, M. A., Thompson, M., van der Lei, J., van Mulligen, E., Velterop, J., Waagmeester, A., Wittenburg, P., Wolstencroft, K., Zhao, J. & Mons, B., 15 Mar 2016, In : Scientific data. 3, 9 p., 160018.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

AstraZeneca-Sanger Drug Combinatio, 17 Jun 2019, In : Nature Communications. 10, 17 p., 2674.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Comparative proteomic analysis of human mesenchymal stromal cell behavior on calcium phosphate ceramics with different osteoinductive potential

Othman, Z., Mohren, R. J. C., Cillero-Pastor, B., Shen, Z., Lacroix, Y. S. N. W., Guttenplan, A. P. M., Birgani, Z. T., Eijssen, L., Luider, T. M., van Rijt, S. & Habibovic, P., Jun 2020, In : Materials today. Bio. 7, 15 p., 100066.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access